Re: mercury 9.8 should crankcase get hot?
Don't know your engine, therefore don't know what to recommend over what you have suggested.
I'd find out if it has a thermostat and/or water pressure bypass valve in the head. If so, remove temporarily, look for good water circulation (running at idle on muffs) and inspect/replace both if any damage is suspected. The stat can be tested on the stove in a pot of water with a candy therm. Opening temp is stamped on the pellet.
140 degrees F is the temperature of most domestic hot water heaters set to the Normal position. If you have such, feel that water.
T stats in 2 current engines here are fitted with 120F and 143F stats. Considering operation, output water, could be at that temp or slightly higher considering this is where the stat starts opening.
Some engines put the pee tube in the exhaust manifold water jacket or at the outlet of the block water, and others take it off the head at the output of the tstat.....in this type, you don't get pee till the stat opens....very bad design.
Cylinder explosion/combustion is what normally generates heat so the hot spots are usually cylinder associated. Therefore mfgrs put cooling passages around those areas, not fuel/air intakes where there is no combustion.
Water to the exhaust manifold has to be there as long as the engine is running so it will go from cool to warm as the engine warms. The stat has nothing (directly) to do with that water. You can just follow the hose to see where it come from. Stats and bypass valves are in the head.
The fact that the intake area of your engine is hotter than the output seems very peculiar to me. You are in the area of engine bearings associated with the crank, reed valves, and the carbs, none of which should be generating any heat.
Best I can do from here.
Mark